title: Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds.
abstract: We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
authors.affiliation: Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
authors.forename: Akika
authors.initials: A
authors.lastname: Futamura
authors.forename: Asuka
authors.initials: A
authors.lastname: Uemura
authors.forename: Takeshi
authors.initials: T
authors.lastname: Imoto
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kitamura
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Matsuura
authors.forename: Chun-Xia
authors.initials: CX
authors.lastname: Wang
authors.forename: Toshiki
authors.initials: T
authors.lastname: Ichihashi
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Sato
authors.forename: Norio
authors.initials: N
authors.lastname: Teramae
authors.forename: Seiichi
authors.initials: S
authors.lastname: Nishizawa
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Ihara
mesh_terms: D001483:Base Sequence; D015374:Biosensing Techniques; D004247:DNA / Q000032:analysis*; D015195:Drug Design; D005456:Fluorescent Dyes / Q000737:chemistry*; D008024:Ligands; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000032:analysis*; D044366:Transition Temperature; D047392:beta-Cyclodextrins / Q000737:chemistry*
chemical_list: D005456:Fluorescent Dyes; D008024:Ligands; D009841:Oligonucleotides; D047392:beta-Cyclodextrins; D012313:RNA; D004247:DNA; C031215:betadex
keywords: DNA recognition; biosensors; cyclodextrin; fluorescence; host-guest systems